LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls

variable        b index 0

variable        x index 50
variable        y index 20
variable        d index 20
variable        v index 5
variable        w index 2

units           lj
dimension       2
atom_style      bond
boundary        f f p

lattice         hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region          box block 0 $x 0 $y -0.5 0.5
region          box block 0 50 0 $y -0.5 0.5
region          box block 0 50 0 20 -0.5 0.5
create_box      1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
  2 by 2 by 1 MPI processor grid
region          circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region          circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region          circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region          circle sphere 11 6.7735026918962581988 0.0 10
create_atoms    1 region circle
Created 361 atoms
  using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
  create_atoms CPU = 0.001 seconds
mass            1 1.0

velocity        all create 0.5 87287 loop geom
velocity        all set $v $w 0 sum yes
velocity        all set 5 $w 0 sum yes
velocity        all set 5 2 0 sum yes

pair_style      lj/cut 2.5
pair_coeff      1 1 10.0 1.0 2.5

bond_style      harmonic
bond_coeff      1 10.0 1.2

# need to preserve 1-3, 1-4 pairwise interactions during hard collisions

special_bonds   lj/coul 0 1 1
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     0 = max # of 1-2 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
create_bonds    many all all 1 1.0 1.5
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 42 29 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard
Added 1014 bonds, new total = 1014
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     6 = max # of 1-2 neighbors
     6 = max # of special neighbors
  special bonds CPU = 0.000 seconds

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 all nve

fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5

comm_style      tiled
comm_modify     cutoff 10.0   # because bonds stretch a long ways
fix             10 all balance 50 0.9 rcb

#compute         1 all property/atom proc
#variable        p atom (c_1%10)+1
#dump            2 all custom 50 tmp.dump id v_p x y z

#dump            3 all image 50 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}

thermo_style    custom step temp epair press f_10[3] f_10
thermo          100
timestep        0.001

run             10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 10
  binsize = 1.4, bins = 42 29 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.123 | 5.142 | 5.176 Mbytes
   Step          Temp          E_pair         Press         f_10[3]          f_10     
         0   25.701528     -2.2032569      3.1039469      3.2354571      1.0526316    
       100   25.57187      -2.2902218      2.9990153      1.0526316      1.0193906    
       200   25.532511     -2.5273097      2.8286231      1.0526316      1.0083102    
       300   25.860246     -3.0674998      2.6725358      1.0415512      1.0083102    
       400   26.628011     -4.394738       2.6618897      1.0526316      1.0083102    
       500   27.627309     -6.2305012      2.6564278      1.0415512      1.0083102    
       600   28.881803     -8.2757766      2.8249236      1.0526316      1.0083102    
       700   29.941402     -9.9816088      2.9828232      1.0526316      1.0083102    
       800   31.118457     -12.199787      3.2044549      1.0304709      1.0083102    
       900   32.393498     -14.204491      2.9496587      1.0747922      1.0193906    
      1000   33.392657     -15.747519      3.1613807      1.0637119      1.0193906    
      1100   34.671769     -17.728904      3.019138       1.0526316      1.0193906    
      1200   35.632627     -19.846347      3.1061176      1.0637119      1.0193906    
      1300   36.77272      -21.156179      3.2353009      1.0415512      1.0193906    
      1400   38.241608     -22.744765      4.1163075      1.0637119      1.0083102    
      1500   40.072478     -25.139827      5.3032535      1.0415512      1.0193906    
      1600   40.665382     -25.901697      5.4330761      1.0858726      1.0083102    
      1700   40.957034     -26.28667       7.1881521      1.1080332      1.0083102    
      1800   41.536831     -27.393841      6.6814405      1.0969529      1.0193906    
      1900   41.952676     -28.123051      7.4683871      1.0858726      1.0193906    
      2000   42.201937     -28.685743      7.4624284      1.0747922      1.0083102    
      2100   41.509082     -27.909225      6.8666955      1.0969529      1.0083102    
      2200   40.794912     -27.085519      5.259945       1.0415512      1.0083102    
      2300   38.749709     -25.14601       4.2936222      1.0526316      1.0083102    
      2400   38.418065     -24.593596      3.1418049      1.1191136      1.0083102    
      2500   36.932588     -23.407613      1.9397982      1.0637119      1.0083102    
      2600   35.979181     -23.066748      2.1678902      1.0637119      1.0193906    
      2700   35.84858      -22.55645       2.0798013      1.0858726      1.0193906    
      2800   35.795795     -22.092149      2.6849882      1.0637119      1.0193906    
      2900   35.754958     -21.662138      2.4892921      1.0526316      1.0083102    
      3000   36.548644     -21.943203      2.8497192      1.0747922      1.0083102    
      3100   36.755531     -22.081384      3.6960187      1.0858726      1.0193906    
      3200   36.606921     -22.538438      3.7047874      1.0415512      1.0193906    
      3300   37.185396     -23.077004      3.4202006      1.0858726      1.0083102    
      3400   37.136687     -23.617745      2.9763794      1.0858726      1.0083102    
      3500   37.908279     -24.364631      3.5155218      1.0304709      1.0083102    
      3600   38.459203     -25.01024       4.3313693      1.0747922      1.0083102    
      3700   39.108683     -25.636756      4.4707992      1.0415512      1.0083102    
      3800   38.67059      -25.126486      5.3753987      1.0747922      1.0083102    
      3900   38.395639     -25.140269      5.1661495      1.0858726      1.0193906    
      4000   38.552057     -24.871721      5.0206769      1.0747922      1.0083102    
      4100   39.065683     -25.344035      4.4042913      1.0858726      1.0083102    
      4200   37.714294     -24.728278      5.1978439      1.0304709      1.0083102    
      4300   38.785555     -25.380643      3.7033369      1.0304709      1.0193906    
      4400   38.341445     -25.13442       3.4298833      1.1191136      1.0193906    
      4500   37.720522     -24.702087      3.4450752      1.0637119      1.0083102    
      4600   37.509806     -24.477444      3.6155741      1.0858726      1.0083102    
      4700   37.319957     -23.722654      4.7111338      1.0526316      1.0193906    
      4800   38.233154     -24.653472      4.25263        1.0637119      1.0083102    
      4900   37.309164     -24.21353       4.8513758      1.0637119      1.0193906    
      5000   37.559292     -24.720651      5.409312       1.0415512      1.0193906    
      5100   37.449783     -25.21538       6.0099692      1.0747922      1.0083102    
      5200   38.187982     -25.16709       6.1425844      1.0415512      1.0083102    
      5300   36.91668      -24.616017      4.7873357      1.0304709      1.0083102    
      5400   35.103465     -23.85158       5.1950262      1.0304709      1.0193906    
      5500   35.299351     -23.946174      4.8038223      1.0526316      1.0083102    
      5600   35.713482     -24.962908      3.5111314      1.0193906      1.0193906    
      5700   33.740794     -23.77699       4.5783011      1.0304709      1.0193906    
      5800   33.791635     -23.536627      3.1317306      1.0415512      1.0193906    
      5900   34.039769     -23.068008      4.0189755      1.0415512      1.0083102    
      6000   32.809103     -22.085195      4.0827943      1.0637119      1.0193906    
      6100   32.522642     -21.979287      4.1437901      1.0637119      1.0083102    
      6200   32.347924     -21.661359      4.1436759      1.0526316      1.0193906    
      6300   32.099974     -21.114688      5.5745084      1.0193906      1.0193906    
      6400   33.767704     -23.489786      4.1038662      1.0526316      1.0193906    
      6500   32.283906     -22.076822      7.2664805      1.0526316      1.0083102    
      6600   33.25146      -23.191973      6.01093        1.0526316      1.0083102    
      6700   31.7665       -22.1476        6.4256074      1.0747922      1.0193906    
      6800   30.775727     -21.513059      5.1709188      1.0304709      1.0083102    
      6900   30.964501     -21.153634      5.1077701      1.0193906      1.0193906    
      7000   31.292268     -20.800916      3.6047789      1.0193906      1.0193906    
      7100   31.460811     -20.280043      3.2369395      1.0193906      1.0083102    
      7200   30.871387     -19.340893      2.9615798      1.0193906      1.0083102    
      7300   28.983475     -18.709174      3.1686601      1.0304709      1.0083102    
      7400   28.032829     -18.200801      1.8738157      1.0304709      1.0193906    
      7500   28.088176     -17.117863      3.5604961      1.0304709      1.0083102    
      7600   27.456327     -17.011025      1.7822114      1.0526316      1.0304709    
      7700   26.483887     -16.024179      1.258431       1.0415512      1.0193906    
      7800   26.023393     -15.532176      1.3663841      1.0304709      1.0083102    
      7900   26.154386     -14.738286      1.5214339      1.0415512      1.0193906    
      8000   25.755121     -14.487715      1.0185064      1.0415512      1.0304709    
      8100   25.468927     -14.273205      1.3553057      1.0526316      1.0304709    
      8200   25.74216      -14.606852      0.13693979     1.0193906      1.0083102    
      8300   24.457219     -14.529941     -0.0032579349   1.0304709      1.0193906    
      8400   24.054076     -13.704387      0.80714443     1.0193906      1.0193906    
      8500   23.742098     -13.699968      0.41096573     1.0304709      1.0193906    
      8600   24.060806     -13.289555      0.22489663     1.0193906      1.0083102    
      8700   23.831533     -13.025052     -0.090244538    1.0304709      1.0193906    
      8800   23.823082     -13.407662     -0.28029605     1.0304709      1.0083102    
      8900   23.982182     -12.862338      0.50556065     1.0193906      1.0193906    
      9000   24.876045     -13.400416      1.1475671      1.0415512      1.0193906    
      9100   25.018155     -13.625286      0.74749825     1.0304709      1.0083102    
      9200   25.671195     -13.850993      0.88340554     1.0526316      1.0083102    
      9300   26.076502     -13.935292      1.2705214      1.0526316      1.0083102    
      9400   25.847786     -13.626034      1.5676611      1.0415512      1.0193906    
      9500   25.963986     -14.23672       1.4791684      1.0304709      1.0083102    
      9600   26.58066      -14.74703       1.3431841      1.0526316      1.0083102    
      9700   27.401448     -14.568412      2.4488742      1.0747922      1.0083102    
      9800   27.927894     -15.254362      2.8516414      1.0415512      1.0083102    
      9900   28.204891     -15.219892      3.0631109      1.0415512      1.0083102    
     10000   27.30902      -14.939134      2.8235246      1.0304709      1.0083102    
Loop time of 0.317224 on 4 procs for 10000 steps with 361 atoms

Performance: 2723630.892 tau/day, 31523.506 timesteps/s, 11.380 Matom-step/s
89.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.066318   | 0.073612   | 0.081352   |   2.6 | 23.21
Bond    | 0.01886    | 0.020483   | 0.022893   |   1.1 |  6.46
Neigh   | 0.051128   | 0.052747   | 0.054345   |   0.5 | 16.63
Comm    | 0.093881   | 0.11329    | 0.13156    |   4.2 | 35.71
Output  | 0.0011573  | 0.0013205  | 0.0016444  |   0.5 |  0.42
Modify  | 0.025957   | 0.026647   | 0.027249   |   0.3 |  8.40
Other   |            | 0.02913    |            |       |  9.18

Nlocal:          90.25 ave          91 max          89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost:         260.75 ave         265 max         256 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs:          889.5 ave        1035 max         794 min
Histogram: 1 1 0 0 1 0 0 0 0 1

Total # of neighbors = 3558
Ave neighs/atom = 9.8559557
Ave special neighs/atom = 5.6177285
Neighbor list builds = 1192
Dangerous builds = 0
Total wall time: 0:00:00
